If this whole problem started when you started dicking with the driveshaft, I'd have to say that is the root of the problem. That being said, you may have related problems.
First, the driveshaft needs to be straight or you will have thrumming, thumping, vibration, etc. Lots of smarter people than me have posted about this (I know C.D. has several posts about this) and you should search for that one. The basic idea is: it should be a straight shot in both axes from the transmission output to diff input. You can imagine the issues if this isn't the case.
Second, the shifter is mounted to the transmission via a platform attached to bushings. I'd guess your bushings are SHOT if this vibration is bad enough that you can't touch the shifter at 50. Easy, cheap fix. Again, though, something has to generate this vibration to transmit to your shifter, so attack the root problem first.